We Rebuild Inside, Then Out
by CayshaGriffin
Summary: You need to rebuild yourself before you can rebuild a world. Sam has to help Tron remember how to trust and forgive before they can make the Grid what it was always supposed to be. Slowly progressing Tron/Sam.
1. Chapter 1

Disclaimer: Tron and all the characters in the movie belong to Disney. I just like to play with them on occasion.

A/N: This is a slow growing Tron/Sam story. So for anyone who doesn't like slash, I suggest you don't read on. For those who are looking for PWP, you won't find that here either. Thanks for reading on if you do. :3

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><p>The circuits that race up and down the programs suit are a firework riot of flickering red and white lights when Sam finds him.<p>

After a week of searching, the User almost gave up. Quorra hadn't been as believing in the old programs survival rates, saying the Sea of Simulation had no doubt swallowed him up or he'd been derezzed along with Clu and Flynn. She wasn't unkind, just matter of fact and sympathetic. But Sam had been stubbornly optimistic.

But finding a barely lit mess that was both Rinzler and Tron all at once made Sam wonder what he could do for his fathers once upon a time best friend. That self-doubt was a taunt though, growing in Sam's belly until it became a challenge to himself as he dragged the program out of the sea's shallows and onto the craggy shore to crouch beside the unresponsive body.

"How do I fix a program corrupted twenty years ago, huh?" He wondered out loud, looking down at his helmeted patient.

Rolling the program onto his side, Sam detached the identity disk and activated it, letting the code stream up and out like modern art in computer code, the DNA that made up each program. It should have been Alan's clean cut code and data and it was still there, intact. But the hack job done to the programs original code made Sam want to wretch. It was less a reprogramming and more like a hostile take over. It was a miracle Tron managed to break through Rinzler even for those few minutes to save them all.

Letting the disk sit on Tron's chest, the code lit up the User's face, reflecting in his eyes. Only then did Sam sigh heavily.

"Here goes."

It took hours that Sam could count and then he simply lost track of time as he slowly, carefully picked the entwined lines of code apart and tossed away the trash that had morphed the Grids champion into Clu's vicious lapdog. Sam saved what he could of Tron's original code, but some still had to be rewritten from what he'd studied from Alan's old work. Other times, Sam just had to wing it.

The behavioral department was easy to clean up, but it was Tron's memory data that made Sam pause. It was layers upon layer of blue code with red so tightly wound around it that removing it would change who Tron was too completely. As much as Sam wanted to save the program that had been his childhood hero for the past twenty years, he wasn't about to play God. Even to save Tron from his memories.

By the time Sam finished his legs ache from kneeling on the hard ground, his skin cold from Tron's wet upper body resting against his thighs. Only after he closes the disk down do Sam's fingers move from the pulse point he'd found just under the rim of the programs helmet, the steady beat had kept him company through his work. But now was the moment of truth. Sliding out from under the program, Sam reattached the disk and watched with a mixture of anticipation and apprehension as the new code uploaded.

When the last kilobyte finally settled in, the program arched, a rasping gasp reverberating through the helmet still in place. Sam moved forward quickly, putting a hand out to reassure as he'd done when Quorra rebooted. But the moment his hand touched the programs suit it lit up bright enough to make Sam squint and shield his eyes. When his vision adjusted it was very clear that something was wrong. One half of Tron's bodysuit was a blinding white, the other half a molten red.

Sam leaned forward to get a closer look, but there was no time when a hand fisted painfully in his short hair and dragged him directly towards the blurring, blinding path of an activated light disk. A murderous pair of eyes , one red, the other blue glared at Sam with clear intent to end the User in his grip. And with alarming clarity, Sam realized he hadn't named this almost composite program. What did you call a new collection of data who'd been to hell and back and still managed to help save the world?

"Tron!" Sam shouted, eyes slamming shut tight as he waited for the pain that would end him.

A few heartbeats later he could hear the disk just under his chin, but no pain followed. In fact, nothing happened and only after Sam relearned the art of breathing did he manage to crack one eye open and then the other when he saw the look of shock and disbelief on Tron's face.

"…Sam?"

The voice was rough with disuse, but it was still familiar in an eerie way. In fact, Tron looked and sounded so much like Alan the first time Sam showed up with a broken arm and a sloppy grin that it was suddenly very awkward rather then alarming.

Sam let out a rush of air he never remembered holding in. "Yeah, hi." He said with a weak grin.

How Tron knew his name was a mystery. Either it was memories from his time as Rinzler or his dad had been really chatty about his real world life.

Either way it wasn't important when, as Sam watched, the red slowly started to fade from Tron's eye and circuits. It was the same moment the security program realized he had an active light disk to the throat of Kevin Flynn's son. Tron pulled back like touching Sam burned, light disk deactivating as it hit the ground while the program stumbled to his feet. He didn't manage to maintain any semblance of balance for long.

Sam quickly shot up to his feet, two hands grasping Tron's upper arms before he could crumple to the ground and pressing his hip into the programs to keep his knees from buckling. When Tron tried to jerk back on instinct, Sam held tighter.

"Whoa! Take it easy. We're good, okay…Just, calm down for a second before you fry all the new wiring." He said with a forced little laugh, trying to assure the still discombobulated program.

Those glowing blue eyes looked at Sam wearily, but leaned against the support he was being given, hands grasping the User's shoulders to give off the illusion of balance regained. Sam didn't buy it and only loosened his grip rather then let go. Still, Tron straightened to his full, straight height with Sam as his minor crutch and the younger Flynn felt the old childhood admiration for the program flicker to life.

"Clu?" Tron asked hesitantly and if not in his stance, Sam could hear the exhaustion in that voice.

"Gone…" Sam paused for a moment and those perceptive eyes narrowed but waited silently for the User to continue. "Dad too."

Tron exhaled heavily as his eyes slid shut, grip tighter on Sam's shoulders for a moment. All the grief the program was willing to show. It was more then Sam ever expected to see. "Flynn…" Tron shook his head. "Reintegration."

It wasn't a question. Sam nodded all the same.

A long silence followed and after a moment, Sam started to feel Tron's weight pressing down on him. Readjusting, he pulled a lightcycle baton from the holster on his calf. Tron stared at it a moment.

"Think you can ride?" Sam asked with a raised brow. It sounded like a dare.

Tron gave a small snort and grabbed the baton, trying to take one confident stride forward and immediately crumpled with an undignified grunt.

Sam sighed and rolled his eyes before grabbing one of Tron's arms and slinging it over his shoulders to get the program back to his feet. Sam gave Tron a smug look.

"Happy now?"

Tron looked at him sidelong. "Yes."

Sam laughed and took the bar from Tron. "Good. But if you tip us over I'm leaving your outdated ass behind."

It got the response Sam was looking for when Tron gave a small growl and a small twitch of his mouth betrayed a restrained smile. "I'll show you outdated, Flynn." One step later, the security program winced. "Later."

Sam just shook his head and chuckled. "I think we're gonna get along just fine."

What the User tried not to focus on was the thin veins of red buried here and there in the blue circuits.

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><p>AN: Reviews are love and keep me going. 3


	2. Chapter 2

Disclaimer: The boys and gal are owned by Disney. I just play with them.

A/N: So I've decided that a post a week sounds reasonable for both you readers and how hectic my normal life is, right? Still, I apologize for not posting sooner and getting sidetracked by making Tron music videos. XD Hope you guys like this chapter, it's more focused on Sam rather then Tron, but it's Sam focusing on Tron. So win-win.

Also, thank you to sharinganavenger for all her help.

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><p>"For being so freakin' compact you weigh a ton." Sam grunted as he half dragged, half carried Tron's unconscious body inside the Grid copy of Flynn's arcade. It was a small favor that no one seemed to run or even visit the place, especially considering his cargo.<p>

Having rebooted the programs system there was still a lot of information for Tron to process, so a few glitches were expected. Hell, Sam figured if someone filled him up with a new mass of information and code with the chest burning qualities associated with a shot of adrenaline straight to the heart then he'd be passed out too.

Of course, that didn't mean Sam had been all that sympathetic when Tron decided to play possum on him during the trip, forcing the user to barely keep them on the lightcycle when the perfectly harmonized motion they'd managed to work out was suddenly thrown off balance by Tron going slack against him. Sam barely got them to Flynn's in an odd jumble of limbs and circuits. Circuits that flared upon contact and made Sam's skin itch under his suit like they'd created a constant loop of energy without an outlet.

It made Sam's blood buzz like he'd just jumped off Encom tower all over again, even after dumping Tron unceremoniously on the curved couch upstairs. The feeling thankfully dissipated quickly when Sam noticed something about Tron's suit. The red veins that had been nagging at the back of Sam's brain the whole trip there…were gone. Leaving Tron's suit a healthy, unblemished blue.

Sam canted his head to the side in bewilderment. "Huh."

Crouching down, he let the ungloved bits of his hand hover just over Tron's mouth and nose, satisfied when he felt a warm rush of air exhaled against his skin. Two fingers to the program's pulse gave Sam a steady heartbeat. That only left one thing to check.

"Okay, lets have one more look under the hood." Sam murmured to himself, mostly to break the unnerving silence as he turned Tron onto his side to access the programs disk.

Last thing he was expecting was a hand that tossed light disks like it was a fine, deadly art to suddenly swat his hand away, making Sam practically jump out of his skin.

But when Sam landed on his ass in surprise, Tron simply let out a groggy mutter and rolled onto his side, showing Sam his back as he made himself comfortable.

Okay, so programs slept. Who knew? Or was it more considered hibernation? Either way it was a relief (even if Sam could still hear the blood pounding in his ears) to know it was something so simple as exhaustion rather then Sam's faulty programming skills. Then Tron made an odd noise that caught the users attention.

Sam nearly lost it a second later when the sound was identified. Because the fearless champion of the Grid, the ex-deadly enforcer known as Rinzler…was purring like a content cat against the cushions. Sam had to slap a hand over his own mouth until the urge to burst out laughing subsided. An action that probably helped him live that much longer in Tron's presence.

Really though, it was a relief to see the program relaxed. Standing up, Sam could only smile faintly at the guy before nodding.

"Get some rest, man. You deserve it."

Sam decided to give the program some privacy. Walking down to the arcade level, the user shook his head with a sigh. "And I really need to stop talking to myself."

Thankfully, the solution to his sad obsession with self communication was only a call away as Sam found an eerie calm in the wash of Grid lights mixed with the familiar glow of an old arcade screen.

She picked up on the second ring.

"…_Cutting it a little close today, Sam. Finally pulled your head out of whatever masterpiece you're building today? Cause I'm starving_..." Quorra replied, her voice a garbled mess over the line. But having just worked out a way to communicate from either side of the laser meant fine tuning it was a ways off.

"Looks like you're gonna have eat without me tonight." Sam threw out there, rather casually. But he pretty much knew the response he'd get.

"…_Sam_…._whatever you've got your head wrapped around can wait till tomorrow. You said we'd try Chinese tonight_…"

Sam had to smile. Even through the messy feed, he could still hear the disappointment in her voice, practically see the childish pout that would accompany it. But Sam would have to be dumb as dirt to miss the concern there too.

"I know. But this is," he looked up at the office. "Really important, okay? I'll make it up to you, but I need another day at least inside. That's what, another half hour tops for you?"

"…_Sam, the Chinese place closes in ten minutes! I'm tired of cheeseburger and Marv_…"

"Quorra. I found him." Sam cut in.

For a moment there was silence, nothing but the crackle of feedback to fill the space.

"…_is he_…?"

Sam let out a sigh at the unspoken question. "Not as bad as we expected. I found him washed up on the shore. I had to play operation with his code, rewrite some of it. Had a hairy couple of minutes there, but it's definitely Tron in control now. I just need time to get him 100% ."

The plea in his voice was clear and he heard Quorra make a noise of disapproval for Sam using it on her. He only had to wait a couple of heartbeats before Quorra sighed.

"…_Eight hours_…" She proposed.

"Twelve." Sam shot back.

"…_Ten_…" The ISO responded firmly, leaving no room for argument. But Sam still had to smile triumphantly with the two extra hours he'd gained . "…_And you better be at that portal when it reopens. Don't be reckless and make me come in after you, Sam Flynn_…" She warned. "..._I'm not happy when I'm left hungry_..."

Sam chuckled. "Deal. Get Marv and me a cheeseburger and I'll throw in some of those cream puffs from the pastry shop when I get back." He promised. The delighted squeak he got in response was agreement enough for him before ending the transmission.

Exhaling slowly, Sam looked up at the office, but there was no sign of movement. Tron was still out then, and that left Sam with a few hours to kill until the program was ready to rejoin the land of the living.

So he took his time inspecting the arcade, thinking maybe his dad had created some new games in an attempt to offer some tailored fun for any of the programs who might have filled the place up at one time. But looking around, all he saw were Galaga and Pac Man machines. Every quarter arcade game Sam could have named from his own childhood crowded around him like old friends. They even sat in the same slots as the arcade back home and it made Sam feel nostalgic. So he sought it out.

It didn't take Sam long, being the one game he and his dad played continuously together. The one game Sam had spent hours and hours trying to beat the older Flynn at. And there it was, sitting in all it's glory a little aways, seperated from the other games. A proud place of honor with it's name scrawled in neon lights on the wall above the console. Tron.

It was ironically amusing really. Even after experiencing the real, blood pounding thing Sam's fingers still itched to get around the joystick and see if that real world experience could get him that high score he'd always coveted.

Sam only got a single step towards the console before his head whipped around at a raw scream that tore through the quiet hums and beeps of old gaming machines.

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><p>AN: Reviews are love and help feed the plot bunnies.


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